Fiber optic biosensors have proven their ability to detect antigens rapidly in a variety of environmental and clinical samples. These biosensors are based on the technique of covalently linking antibodies to the core of an optical fiber and detecting antigen binding via measurement of fluorescence induced in the evanescent wave. One problem associated with these biosensors is the fiber-to-fiber variability in measured signal. We have addressed this problem by labeling a portion of the immobilized capture antibody with the fluorescent cyanine dye Cy5.5 (emission λ m a x = 696 nm). The antigen was then labeled with fluorescent Cy5 (emission λ m a x = 668 nm). Both fluorophores were excited by 635-nm light, and their emission was collected using both a fiber optic spectrometer and a biosensor optimized to collect fluorescence at two wavelengths. The fluorescence from the Cy5.5-labeled capture antibody served as a calibration signal for each fiber and corrected for differences in optics, fiber defects, and varying amounts of capture antibody present on the fiber. Our data show that normalizing the signal measured from Cy5-labeled antigen binding to the Cy5.5 signal provides a standardization process for greatly reducing signal variance among individual fibers.